Self-transport of swimming bacteria is impaired by porous microstructure

Abstract: Motility is a fundamental survival strategy of bacteria to navigate porous environments. Swimming cells thrive in quiescent wetlands and sediments at the bottom of the marine water column, where they mediate many essential biogeochemical processes. While swimming motility in bulk fluid is now well established, a comprehensive understanding of the mechanisms regulating self-transport in the confined interstices of porous media is lacking, and determining the interactions between cells and surfaces of the solid matrix becomes paramount. Here, we precisely track the movement of bacteria (\emph{Magnetococcus marinus}) through a series of microfluidic porous media with broadly varying geometries and show that cell motility results in a succession of scattering events from the porous microstructure. Order or disorder can impact the cells' motility over short ranges, but we directly demonstrate that their large-scale transport properties are regulated by the cutoff of their persistent swimming, which is dictated primarily by the porosity and scale of the porous geometry. The effective mean free path is established as the key geometrical parameter controlling transport, and along with with minimal knowledge of cell swimming motility and surface scattering properties, we implement a theoretical model that universally predicts the effective diffusion of cells for the geometries studied here. These results are an important step toward predicting the physical ecology of swimming cells in quiescent porous media and understanding their role in environmental and health hazards in stagnant water.